Yes. According to how they word it, as long as 45 credits of your second bachelor's degree are completed by November 1, that should be the only cGPA they use. If you've completed 60 credits of your second bachelor's degree, they'll use the cGPA for all 60 credits. In neither case should any of the classes from your first degree factor into your cGPA.
But as for the comparable degree language, I think it refers mostly to your grades. They say "...45 consecutive graded credits (in a second/alternate bachelor's degree program) must be completed by the November 1 application deadline.The remaining 15 (or more) credits must be completed by July 31 of the year of entry to medical school, and these must be at a level comparable to that which appears in the academic records submitted at the time of application."
The "level comparable" refers to the previous 45 credits required to apply based on a second degree. So for example if in November 2020 you want to apply based on a second bachelor's degree, you'd have to have 45 credits of it already completed by November 1. If you do, they'll base your cGPA on only those 45 credits. BUT, you also need to finish the second bachelor's degree before you can actually enrol (i.e. you can't start a second degree, get admitted to med, and then not finish the second degree), so the remaining 15 credits for the second degree would have to be completed in either the Fall or Winter semester. The comparable level language means that if your first 45 credits were at a 4.0 GPA, and they admit you based on that, then they expect you to complete the remaining 15 credits at a level comparable, i.e. if you get a bunch of Bs and Cs in 100 level classes, they'll be like WTF no. In the next sentence on their website they say, "A marked decline in academic performance in the final term(s) may lead to withdrawal of an offer of admission." Which I think supports the interpretation that this policy refers to your actual grades, and not some arbitrary comparison on the relative difficulty of your two bachelor's degrees.
The whole point is that the first bachelor's degree isn't supposed to matter anymore, and McGill isn't like the French schools with some formal published ranking of how they perceive the relative difficulty of all the different undergrad programs.
Maybe I'm mistaken, but this is how I understand it!